Prayer in my mind is no different than someone saying "we'll keep you in our thoughts.", "I hope everything will be okay." Or any variation of that.
If in truth G-d hears prayers and acts on them, hey, no harm, no foul.
If G-d does not, then just the energy of the prayer, thought, vibe, intention, etc can help.
We have a thread in TTC that is called the TTC Prayer List. It is a list of women who are ttc, and want a little extra help. Not everyone on the list believes the same thing, but we all knew what it meant. That there were multiple people out there wishing we would get pregnant.
Certainly no harm in that.
I am with the other posters that if you say "I'll pray for you" and mean to find Jesus or whatever, then yeah, I am a little offended by that. But all in all, it is your time, and your energy....doesn't mean I am going to change my mind on what I believe.
If you want to pray for me, heck the positive energy can't hurt.